The Cell-Chapter 6 and 7

1
The Cell-Chapter 6 and 7

• Key Questions
• What are the structures and functions of cellular
  organelles?
• How does the plasma membrane regulate the
  cellular environment?
• Cell Introduction

2
Cells

• All organisms are made of cells
• The cell is the simplest collection of matter
  that can be alive
• Cell structure is correlated to cellular function
• All cells are related by their descent from
  earlier cells

3
Figure 6.1
4
Figure 6.2b
1 cm
Frog egg
1 mm
Human egg
100 ?m
Most plant andanimal cells
Light microscopy
10 ?m
Nucleus
Most bacteria
Mitochondrion
1 ?m
Smallest bacteria
Super-resolutionmicroscopy
100 nm
Viruses
Electron microscopy
Ribosomes
10 nm
Proteins
Lipids
1 nm
Small molecules
Atoms
0.1 nm
5
Figure 6.3
Electron Microscopy (EM)
Light Microscopy (LM)
Brightfield
Cross sectionof cilium
Longitudinal sectionof cilium
Confocal
(unstained specimen)
Cilia
50 ?m
Brightfield
(stained specimen)
50 ?m
2 ?m
2 ?m
Transmission electronmicroscopy (TEM)
Scanning electronmicroscopy (SEM)
Deconvolution
Phase-contrast
10 ?m
Differential-interference-contrast (Nomarski)
Super-resolution
Fluorescence
1 ?m
10 ?m
6
Eukaryotic cells have internal membranes that
compartmentalize their functions

• The basic structural and functional unit of every
  organism is one of two types of cells
  prokaryotic or eukaryotic
• Only organisms of the domains Bacteria and
  Archaea consist of prokaryotic cells
• Protists, fungi, animals, and plants all consist
  of eukaryotic cells

7
Comparing Prokaryotic and Eukaryotic Cells

• Basic features of all cells
• Plasma membrane
• Semifluid substance called cytosol
• Chromosomes (carry genes)
• Ribosomes (make proteins)

8

• Prokaryotic cells are characterized by having
• No nucleus
• DNA in an unbound region called the nucleoid
• No membrane-bound organelles
• Cytoplasm bound by the plasma membrane

9
Figure 6.5
Fimbriae
Nucleoid
Ribosomes
Plasmamembrane
Bacterialchromosome
Cell wall
Capsule
0.5 ?m
Flagella
(b)
(a)
A typicalrod-shapedbacterium
A thin sectionthrough thebacterium
Bacilluscoagulans (TEM)
10

• Eukaryotic cells are characterized by having
• DNA in a nucleus that is bounded by a membranous
  nuclear envelope
• Membrane-bound organelles
• Cytoplasm in the region between the plasma
  membrane and nucleus
• Eukaryotic cells are generally much larger than
  prokaryotic cells

11

• The plasma membrane is a selective barrier that
  allows sufficient passage of oxygen, nutrients,
  and waste to service the volume of every cell
• The general structure of a biological membrane is
  a double layer of phospholipids

12
Figure 6.6
(a)
TEM of a plasmamembrane
Outside of cell
Inside of cell
0.1 ?m
Carbohydrate side chains
Hydrophilicregion
Hydrophobicregion
Hydrophilicregion
Phospholipid
Proteins
(b) Structure of the plasma membrane
13

• Metabolic requirements set upper limits on the
  size of cells
• The surface area to volume ratio of a cell is
  critical
• As the surface area increases by a factor of n2,
  the volume increases by a factor of n3
• Small cells have a greater surface area relative
  to volume

14
Figure 6.7
Surface area increases whiletotal volume remains
constant
5
1
1
Total surface areasum of the surface
areas(height ? width) of all boxsides ? number
of boxes
6
150
750
Total volumeheight ? width ? length? number of
boxes
125
125
1
Surface-to-volume(S-to-V) ratiosurface area ?
volume
1.2
6
6
15
A Panoramic View of the Eukaryotic Cell

• A eukaryotic cell has internal membranes that
  partition the cell into organelles
• Plant and animal cells have most of the same
  organelles

16
Figure 6.8a
ENDOPLASMIC RETICULUM (ER)
Nuclearenvelope
SmoothER
RoughER
Flagellum
NUCLEUS
Nucleolus
Chromatin
Centrosome
Plasmamembrane
CYTOSKELETON
Microfilaments
Intermediate filaments
Microtubules
Ribosomes
Microvilli
Golgi apparatus
Peroxisome
Lysosome
Mitochondrion
17
Figure 6.8b
Animal Cells
Fungal Cells
1 ?m
Parentcell
10 ?m
Cell wall
Vacuole
Buds
Cell
5 ?m
Nucleus
Nucleus
Nucleolus
Mitochondrion
Human cells from liningof uterus (colorized TEM)
Yeast cells budding(colorized SEM)
A single yeast cell(colorized TEM)
18
Figure 6.8c
Nuclearenvelope
Roughendoplasmicreticulum
Smoothendoplasmicreticulum
NUCLEUS
Nucleolus
Chromatin
Ribosomes
Central vacuole
Golgiapparatus
Microfilaments
Intermediatefilaments
CYTOSKELETON
Microtubules
Mitochondrion
Peroxisome
Chloroplast
Plasma membrane
Cell wall
Plasmodesmata
Wall of adjacent cell
19
Figure 6.8d
Plant Cells
Protistan Cells
Flagella
Cell
1 ?m
5 ?m
8 ?m
Cell wall
Nucleus
Chloroplast
Nucleolus
Mitochondrion
Vacuole
Nucleus
Nucleolus
Chloroplast
Chlamydomonas(colorized SEM)
Cells from duckweed(colorized TEM)
Cell wall
Chlamydomonas(colorized TEM)
20
The eukaryotic cells genetic instructions are
housed in the nucleus and carried out by the
ribosomes

• The nucleus contains most of the DNA in a
  eukaryotic cell
• Ribosomes use the information from the DNA to
  make proteins

21
The Nucleus Information Central

• The nucleus contains most of the cells genes and
  is usually the most conspicuous organelle
• The nuclear envelope encloses the nucleus,
  separating it from the cytoplasm
• The nuclear membrane is a double membrane each
  membrane consists of a lipid bilayer

22
Figure 6.9
1 ?m
Nucleus
Nucleolus
Chromatin
Nuclear envelope
Inner membrane
Outer membrane
Nuclear pore
Rough ER
Porecomplex
Surface of nuclearenvelope
Ribosome
Close-upof nuclearenvelope
Chromatin
0.25 ?m
1 ?m
Pore complexes (TEM)
Nuclear lamina (TEM)
23

• Pores regulate the entry and exit of molecules
  from the nucleus
• The shape of the nucleus is maintained by the
  nuclear lamina, which is composed of protein

24

• In the nucleus, DNA is organized into discrete
  units called chromosomes
• Each chromosome is composed of a single DNA
  molecule associated with proteins
• The DNA and proteins of chromosomes are together
  called chromatin
• Chromatin condenses to form discrete chromosomes
  as a cell prepares to divide
• The nucleolus is located within the nucleus and
  is the site of ribosomal RNA (rRNA) synthesis

25
Ribosomes Protein Factories

• Ribosomes are particles made of ribosomal RNA and
  protein
• Ribosomes carry out protein synthesis in two
  locations
• In the cytosol (free ribosomes)
• On the outside of the endoplasmic reticulum or
  the nuclear envelope (bound ribosomes)

26
Figure 6.10
0.25 ?m
Free ribosomes in cytosol
Endoplasmic reticulum (ER)
Ribosomes bound to ER
Largesubunit
Smallsubunit
TEM showing ER andribosomes
Diagram of a ribosome
27
The endomembrane system regulates protein traffic
and performs metabolic functions in the cell

• Components of the endomembrane system
• Nuclear envelope
• Endoplasmic reticulum
• Golgi apparatus
• Lysosomes
• Vacuoles
• Plasma membrane
• These components are either continuous or
  connected via transfer by vesicles

28
The Endoplasmic Reticulum Biosynthetic Factory

• The endoplasmic reticulum (ER) accounts for more
  than half of the total membrane in many
  eukaryotic cells
• The ER membrane is continuous with the nuclear
  envelope
• There are two distinct regions of ER
• Smooth ER, which lacks ribosomes
• Rough ER, surface is studded with ribosomes

29
Figure 6.11
Smooth ER
Nuclearenvelope
Rough ER
ER lumen
Cisternae
Transitional ER
Ribosomes
Transport vesicle
200 nm
Rough ER
Smooth ER
30
Functions of Smooth ER

• The smooth ER
• Synthesizes lipids
• Metabolizes carbohydrates
• Detoxifies drugs and poisons
• Stores calcium ions

Functions of Rough ER

• The rough ER
• Has bound ribosomes, which secrete glycoproteins
  (proteins covalently bonded to carbohydrates)
• Distributes transport vesicles, proteins
  surrounded by membranes
• Is a membrane factory for the cell

31
The Golgi Apparatus Shipping and Receiving
Center

• The Golgi apparatus consists of flattened
  membranous sacs called cisternae
• Functions of the Golgi apparatus
• Modifies products of the ER
• Manufactures certain macromolecules
• Sorts and packages materials into transport
  vesicles

32
Figure 6.12
cis face(receiving side ofGolgi apparatus)
0.1 ?m
Cisternae
trans face(shipping side ofGolgi apparatus)
TEM of Golgi apparatus
33
Lysosomes Digestive Compartments

• A lysosome is a membranous sac of hydrolytic
  enzymes that can digest macromolecules
• Lysosomal enzymes can hydrolyze proteins, fats,
  polysaccharides, and nucleic acids
• Lysosomal enzymes work best in the acidic
  environment inside the lysosome

34

• Some types of cell can engulf another cell by
  phagocytosis this forms a food vacuole
• A lysosome fuses with the food vacuole and
  digests the molecules
• Lysosomes also use enzymes to recycle the cells
  own organelles and macromolecules, a process
  called autophagy

35
Figure 6.13
Vesicle containingtwo damagedorganelles
1 ?m
Nucleus
1 ?m
Mitochondrionfragment
Lysosome
Peroxisomefragment
Digestiveenzymes
Lysosome
Lysosome
Peroxisome
Plasma membrane
Digestion
Food vacuole
Digestion
Mitochondrion
Vesicle
(a) Phagocytosis
(b) Autophagy
36
Vacuoles Diverse Maintenance Compartments

• A plant cell or fungal cell may have one or
  several vacuoles, derived from endoplasmic
  reticulum and Golgi apparatus

• Food vacuoles are formed by phagocytosis
• Contractile vacuoles, found in many freshwater
  protists, pump excess water out of cells
• Central vacuoles, found in many mature plant
  cells, hold organic compounds and water

37
Figure 6.14
Central vacuole
Cytosol
Centralvacuole
Nucleus
Cell wall
Chloroplast
5 ?m
38
The Endomembrane System A Review

• The endomembrane system is a complex and dynamic
  player in the cells compartmental organization

39
Figure 6.15-3
Nucleus
Rough ER
Smooth ER
cis Golgi
Plasmamembrane
trans Golgi
40
Mitochondria and chloroplasts change energy from
one form to another

• Mitochondria are the sites of cellular
  respiration, a metabolic process that uses oxygen
  to generate ATP
• Chloroplasts, found in plants and algae, are the
  sites of photosynthesis
• Peroxisomes are oxidative organelles

41
The Evolutionary Origins of Mitochondria and
Chloroplasts

• Mitochondria and chloroplasts have similarities
  with bacteria
• Enveloped by a double membrane
• Contain free ribosomes and circular DNA molecules
• Grow and reproduce somewhat independently in cells

42

• The Endosymbiont theory
• An early ancestor of eukaryotic cells engulfed a
  nonphotosynthetic prokaryotic cell, which formed
  an endosymbiont relationship with its host
• The host cell and endosymbiont merged into a
  single organism, a eukaryotic cell with a
  mitochondrion
• At least one of these cells may have taken up a
  photosynthetic prokaryote, becoming the ancestor
  of cells that contain chloroplasts

43
Figure 6.16
Nucleus
Endoplasmicreticulum
Engulfing of oxygen-using nonphotosyntheticproka
ryote, whichbecomes a mitochondrion
Nuclear envelope
Ancestor ofeukaryotic cells(host cell)
Mitochondrion
Engulfing ofphotosyntheticprokaryote
At leastone cell
Chloroplast
Nonphotosyntheticeukaryote
Mitochondrion
Photosynthetic eukaryote
44
Mitochondria Chemical Energy Conversion

• Mitochondria are in nearly all eukaryotic cells
• They have a smooth outer membrane and an inner
  membrane folded into cristae
• The inner membrane creates two compartments
  intermembrane space and mitochondrial matrix
• Some metabolic steps of cellular respiration are
  catalyzed in the mitochondrial matrix
• Cristae present a large surface area for enzymes
  that synthesize ATP

45
Figure 6.17
10 ?m
Intermembrane space
Mitochondria
Outer
membrane
DNA
Inner
MitochondrialDNA
membrane
Freeribosomesin themitochondrialmatrix
Cristae
Nuclear DNA
Matrix
0.1 ?m
(b)
Network of mitochondria in a protistcell (LM)
(a) Diagram and TEM of mitochondrion
46
Chloroplasts Capture of Light Energy

• Chloroplasts contain the green pigment
  chlorophyll, as well as enzymes and other
  molecules that function in photosynthesis
• Chloroplasts are found in leaves and other green
  organs of plants and in algae

• Chloroplast structure includes
• Thylakoids, membranous sacs, stacked to form a
  granum
• Stroma, the internal fluid
• The chloroplast is one of a group of plant
  organelles, called plastids

47
Figure 6.18
50 ?m
Ribosomes
Stroma
Inner and outer
membranes
Granum
Chloroplasts(red)
DNA
1 ?m
Intermembrane space
Thylakoid
(a) Diagram and TEM of chloroplast
(b) Chloroplasts in an algal cell
48
Peroxisomes Oxidation

• Peroxisomes are specialized metabolic
  compartments bounded by a single membrane
• Peroxisomes produce hydrogen peroxide and convert
  it to water
• Peroxisomes perform reactions with many different
  functions
• How peroxisomes are related to other organelles
  is still unknown

49
Figure 6.19
1 ?m
Chloroplast
Peroxisome
Mitochondrion
50
The cytoskeleton is a network of fibers that
organizes structures and activities in the cell

• The cytoskeleton is a network of fibers extending
  throughout the cytoplasm
• It organizes the cells structures and
  activities, anchoring many organelles
• It is composed of three types of molecular
  structures
• Microtubules
• Microfilaments
• Intermediate filaments

51
Figure 6.20
10 ?m
52
Roles of the Cytoskeleton Support and Motility

• The cytoskeleton helps to support the cell and
  maintain its shape
• It interacts with motor proteins to produce
  motility
• Inside the cell, vesicles can travel along
  monorails provided by the cytoskeleton
• Recent evidence suggests that the cytoskeleton
  may help regulate biochemical activities

53
Figure 6.21
Vesicle
ATP
Receptor formotor protein
Motor protein(ATP powered)
Microtubuleof cytoskeleton
(a)
0.25 ?m
Vesicles
Microtubule
(b)
54
Components of the Cytoskeleton

• Three main types of fibers make up the
  cytoskeleton
• Microtubules are the thickest of the three
  components of the cytoskeleton
• Microfilaments, also called actin filaments, are
  the thinnest components
• Intermediate filaments are fibers with diameters
  in a middle range

55
Table 6.1
5 ?m
10 ?m
10 ?m
Column of tubulin dimers
Keratin proteins
Actin subunit
Fibrous subunit (keratinscoiled together)
25 nm
8?12 nm
7 nm
Tubulin dimer
?
?
56
Microtubules

• Microtubules are hollow rods about 25 nm in
  diameter and about 200 nm to 25 microns long
• Functions of microtubules
• Shaping the cell
• Guiding movement of organelles
• Separating chromosomes during cell division

57

• Centrosomes and Centrioles
• In many cells, microtubules grow out from a
  centrosome near the nucleus
• The centrosome is a microtubule-organizing
  center
• In animal cells, the centrosome has a pair of
  centrioles, each with nine triplets of
  microtubules arranged in a ring

58
Figure 6.22
Centrosome
Microtubule
Centrioles
0.25 ?m
Longitudinalsection ofone centriole
Microtubules
Cross sectionof the other centriole
59

• Cilia and Flagella
• Microtubules control the beating of cilia and
  flagella, locomotor appendages of some cells
• Cilia and flagella differ in their beating
  patterns

60
Figure 6.23
Direction of swimming
(a) Motion of flagella
5 ?m
Direction of organisms movement
Power stroke Recovery stroke
(b) Motion of cilia
15 ?m
61

• Cilia and flagella share a common structure
• A core of microtubules sheathed by the plasma
  membrane
• A basal body that anchors the cilium or flagellum
• A motor protein called dynein, which drives the
  bending movements of a cilium or flagellum

Animation Cilia and Flagella
62
Figure 6.24
0.1 ?m
Plasma membrane
Outer microtubuledoublet
Dynein proteins
Centralmicrotubule
Radialspoke
Microtubules
Cross-linkingproteins betweenouter doublets
(b)
Cross section ofmotile cilium
Plasmamembrane
Basal body
0.1 ?m
0.5 ?m
Longitudinal sectionof motile cilium
(a)
Triplet
(c)
Cross section ofbasal body
63

• How dynein walking moves flagella and cilia
• Dynein arms alternately grab, move, and release
  the outer microtubules
• Protein cross-links limit sliding
• Forces exerted by dynein arms cause doublets to
  curve, bending the cilium or flagellum

64
Figure 6.25
Microtubuledoublets
ATP
Dynein protein
(a) Effect of unrestrained dynein movement
Cross-linking proteinsbetween outer doublets
ATP
Anchoragein cell
(b) Effect of cross-linking proteins
1
3
2
(c) Wavelike motion
65
Microfilaments (Actin Filaments)

• Microfilaments are solid rods about 7 nm in
  diameter, built as a twisted double chain of
  actin subunits
• The structural role of microfilaments is to bear
  tension, resisting pulling forces within the cell
• They form a 3-D network called the cortex just
  inside the plasma membrane to help support the
  cells shape
• Bundles of microfilaments make up the core of
  microvilli of intestinal cells

66
Figure 6.26
Microvillus
Plasma membrane
Microfilaments (actinfilaments)
Intermediate filaments
0.25 ?m
67

• Microfilaments that function in cellular motility
  contain the protein myosin in addition to actin
• In muscle cells, thousands of actin filaments are
  arranged parallel to one another
• Thicker filaments composed of myosin
  interdigitate with the thinner actin fibers

68
Figure 6.27
Muscle cell
0.5 ?m
Actin
filament
Myosin
filament
Myosin
head
(a) Myosin motors in muscle cell contraction
Cortex (outer cytoplasm)gel with actin network
100 ?m
Inner cytoplasm solwith actin subunits
Extendingpseudopodium
(b) Amoeboid movement
Chloroplast
30 ?m
(c) Cytoplasmic streaming in plant cells
69

• Localized contraction brought about by actin and
  myosin also drives amoeboid movement
• Pseudopodia (cellular extensions) extend and
  contract through the reversible assembly and
  contraction of actin subunits into microfilaments

70

• Cytoplasmic streaming is a circular flow of
  cytoplasm within cells
• This streaming speeds distribution of materials
  within the cell
• In plant cells, actin-myosin interactions and
  sol-gel transformations drive cytoplasmic
  streaming

71
Intermediate Filaments

• Intermediate filaments range in diameter from
  812 nanometers, larger than microfilaments but
  smaller than microtubules
• They support cell shape and fix organelles in
  place
• Intermediate filaments are more permanent
  cytoskeleton fixtures than the other two classes

72
Concept 6.7 Extracellular components and
connections between cells help coordinate
cellular activities

• Most cells synthesize and secrete materials that
  are external to the plasma membrane
• These extracellular structures include
• Cell walls of plants
• The extracellular matrix (ECM) of animal cells
• Intercellular junctions

73
Cell Walls of Plants

• The cell wall is an extracellular structure that
  distinguishes plant cells from animal cells
• Prokaryotes, fungi, and some protists also have
  cell walls
• The cell wall protects the plant cell, maintains
  its shape, and prevents excessive uptake of water
• Plant cell walls are made of cellulose fibers
  embedded in other polysaccharides and protein

74

• Plant cell walls may have multiple layers
• Primary cell wall relatively thin and flexible
• Middle lamella thin layer between primary walls
  of adjacent cells
• Secondary cell wall (in some cells) added
  between the plasma membrane and the primary cell
  wall
• Plasmodesmata are channels between adjacent plant
  cells

75
Figure 6.28
Secondarycell wall
Primarycell wall
Middlelamella
1 ?m
Central vacuole
Cytosol
Plasma membrane
Plant cell walls
Plasmodesmata
76
Figure 6.29
RESULTS
10 ?m
Distribution of cellulosesynthase over time
Distribution ofmicrotubulesover time
77
The Extracellular Matrix (ECM) of Animal Cells

• Animal cells lack cell walls but are covered by
  an elaborate extracellular matrix (ECM)
• The ECM is made up of glycoproteins such as
  collagen, proteoglycans, and fibronectin
• ECM proteins bind to receptor proteins in the
  plasma membrane called integrins

78
Figure 6.30
Collagen
Polysaccharidemolecule
EXTRACELLULAR FLUID
Carbo-hydrates
Proteoglycancomplex
Fibronectin
Core protein
Integrins
Proteoglycanmolecule
Plasmamembrane
Proteoglycan complex
CYTOPLASM
Micro- filaments
79

• Functions of the ECM
• Support
• Adhesion
• Movement
• Regulation

80
Cell Junctions

• Neighboring cells in tissues, organs, or organ
  systems often adhere, interact, and communicate
  through direct physical contact
• Intercellular junctions facilitate this contact
• There are several types of intercellular
  junctions
• Plasmodesmata
• Tight junctions
• Desmosomes
• Gap junctions

81
Plasmodesmata in Plant Cells

• Plasmodesmata are channels that perforate plant
  cell walls
• Through plasmodesmata, water and small solutes
  (and sometimes proteins and RNA) can pass from
  cell to cell

82
Figure 6.31
Cell walls
Interiorof cell
Interiorof cell
Plasmodesmata
Plasma membranes
0.5 ?m
83
Tight Junctions, Desmosomes, and Gap Junctions in
Animal Cells

• At tight junctions, membranes of neighboring
  cells are pressed together, preventing leakage of
  extracellular fluid
• Desmosomes (anchoring junctions) fasten cells
  together into strong sheets
• Gap junctions (communicating junctions) provide
  cytoplasmic channels between adjacent cells

84
Figure 6.32
Tight junctions preventfluid from movingacross
a layer of cells
Tight junction
TEM
0.5 ?m
Tight junction
Intermediatefilaments
Desmosome
TEM
1 ?m
Gapjunction
Ions or smallmolecules
Spacebetween cells
TEM
Extracellularmatrix
Plasma membranesof adjacent cells
0.1 ?m
85
The Cell A Living Unit Greater Than the Sum of
Its Parts

• Cells rely on the integration of structures and
  organelles in order to function
• For example, a macrophages ability to destroy
  bacteria involves the whole cell, coordinating
  components such as the cytoskeleton, lysosomes,
  and plasma membrane

86
Figure 6.33
5 ?m